Parses the header section of an ADAT file.
Arguments
- file
Character. The elaborated path and file name of the
*.adatfile to be loaded into an R workspace environment.
Value
A list of relevant file information required by read_adat()
in order to complete loading the ADAT file, including:
- Header.Meta
list of notes and other information about the adat
- Col.Meta
list of vectors that contain the column meta data about individual analytes, includes information about the target name and calibration and QC ratios
- file_specs
list of values of the file parsing specifications
- row_meta
character vector of the clinical variables; assay information that is included in the adat output along with the RFU data
See also
Other IO:
loadAdatsAsList(),
read_adat(),
soma_adat,
write_adat()
Examples
f <- system.file("extdata", "example_data10.adat",
package = "SomaDataIO", mustWork = TRUE)
header <- parseHeader(f)
names(header)
#> [1] "Header.Meta" "Col.Meta" "file_specs" "row_meta"
header$Header.Meta
#> $HEADER
#> $HEADER$AdatId
#> [1] "GID-1234-56-789-abcdef"
#> attr(,"raw_key")
#> [1] "!AdatId"
#>
#> $HEADER$Version
#> [1] "1.2"
#> attr(,"raw_key")
#> [1] "!Version"
#>
#> $HEADER$AssayType
#> [1] "PharmaServices"
#> attr(,"raw_key")
#> [1] "!AssayType"
#>
#> $HEADER$AssayVersion
#> [1] "V4"
#> attr(,"raw_key")
#> [1] "!AssayVersion"
#>
#> $HEADER$AssayRobot
#> [1] "Fluent 1 L-307"
#> attr(,"raw_key")
#> [1] "!AssayRobot"
#>
#> $HEADER$Legal
#> [1] "Experiment details and data have been processed to protect Personally Identifiable Information (PII) and comply with existing privacy laws."
#> attr(,"raw_key")
#> [1] "!Legal"
#>
#> $HEADER$CreatedBy
#> [1] "PharmaServices"
#> attr(,"raw_key")
#> [1] "!CreatedBy"
#>
#> $HEADER$CreatedDate
#> [1] "2020-07-24"
#> attr(,"raw_key")
#> [1] "!CreatedDate"
#>
#> $HEADER$EnteredBy
#> [1] "Technician1"
#> attr(,"raw_key")
#> [1] "!EnteredBy"
#>
#> $HEADER$ExpDate
#> [1] "2020-06-18, 2020-07-20"
#> attr(,"raw_key")
#> [1] "!ExpDate"
#>
#> $HEADER$GeneratedBy
#> [1] "Px (Build: : ), Canopy_0.1.1"
#> attr(,"raw_key")
#> [1] "!GeneratedBy"
#>
#> $HEADER$RunNotes
#> [1] "2 columns ('Age' and 'Sex') have been added to this ADAT. Age has been randomly increased or decreased by 1-2 years to protect patient information"
#> attr(,"raw_key")
#> [1] "!RunNotes"
#>
#> $HEADER$ProcessSteps
#> [1] "Raw RFU, Hyb Normalization, medNormInt (SampleId), plateScale, Calibration, anmlQC, qcCheck, anmlSMP"
#> attr(,"raw_key")
#> [1] "!ProcessSteps"
#>
#> $HEADER$ProteinEffectiveDate
#> [1] "2019-08-06"
#> attr(,"raw_key")
#> [1] "!ProteinEffectiveDate"
#>
#> $HEADER$StudyMatrix
#> [1] "EDTA Plasma"
#> attr(,"raw_key")
#> [1] "!StudyMatrix"
#>
#> $HEADER$PlateType
#> character(0)
#> attr(,"raw_key")
#> [1] "!PlateType"
#>
#> $HEADER$LabLocation
#> [1] "SLUS"
#> attr(,"raw_key")
#> [1] "!LabLocation"
#>
#> $HEADER$StudyOrganism
#> character(0)
#> attr(,"raw_key")
#> [1] "!StudyOrganism"
#>
#> $HEADER$Title
#> [1] "Example Adat Set001, Example Adat Set002"
#> attr(,"raw_key")
#> [1] "!Title"
#>
#> $HEADER$AssaySite
#> [1] "SW"
#> attr(,"raw_key")
#> [1] "!AssaySite"
#>
#> $HEADER$CalibratorId
#> [1] "170261"
#> attr(,"raw_key")
#> [1] "!CalibratorId"
#>
#> $HEADER$ReportConfig
#> [1] "{\"analysisSteps\":[{\"stepType\":\"hybNorm\",\"referenceSource\":\"intraplate\",\"includeSampleTypes\":[\"QC\",\"Calibrator\",\"Buffer\"]},{\"stepName\":\"medNormInt\",\"stepType\":\"medNorm\",\"includeSampleTypes\":[\"Calibrator\",\"Buffer\"],\"referenceSource\":\"intraplate\",\"referenceFields\":[\"SampleId\"]},{\"stepType\":\"plateScale\",\"referenceSource\":\"Reference_v4_Plasma_Calibrator_170261\"},{\"stepType\":\"calibrate\",\"referenceSource\":\"Reference_v4_Plasma_Calibrator_170261\"},{\"stepName\":\"anmlQC\",\"stepType\":\"ANML\",\"effectSizeCutoff\":2.0,\"minFractionUsed\":0.3,\"includeSampleTypes\":[\"QC\"],\"referenceSource\":\"Reference_v4_Plasma_ANML\"},{\"stepType\":\"qcCheck\",\"QCReferenceSource\":\"Reference_v4_Plasma_QC_ANML_170255\",\"tailsCriteriaLower\":0.8,\"tailsCriteriaUpper\":1.2,\"tailThreshold\":15.0,\"QCAdditionalReferenceSources\":[\"Reference_v4_Plasma_QC_ANML_170259\",\"Reference_v4_Plasma_QC_ANML_170260\"],\"prenormalized\":true},{\"stepName\":\"anmlSMP\",\"stepType\":\"ANML\",\"effectSizeCutoff\":2.0,\"minFractionUsed\":0.3,\"includeSampleTypes\":[\"Sample\"],\"referenceSource\":\"Reference_v4_Plasma_ANML\"}],\"qualityReports\":[\"SQS Report\"],\"filter\":{\"proteinEffectiveDate\":\"2019-08-06\"}}"
#> attr(,"raw_key")
#> [1] "!ReportConfig"
#>
#> $HEADER$HybNormReference
#> [1] "intraplate"
#> attr(,"raw_key")
#> [1] "HybNormReference"
#>
#> $HEADER$MedNormReference
#> [1] "intraplate"
#> attr(,"raw_key")
#> [1] "MedNormReference"
#>
#> $HEADER$NormalizationAlgorithm
#> [1] "ANML"
#> attr(,"raw_key")
#> [1] "NormalizationAlgorithm"
#>
#> $HEADER$PlateScale_ReferenceSource
#> [1] "Reference_v4_Plasma_Calibrator_170261"
#> attr(,"raw_key")
#> [1] "PlateScale_ReferenceSource"
#>
#> $HEADER$PlateScale_Scalar_Example_Adat_Set001
#> [1] "1.08091554"
#> attr(,"raw_key")
#> [1] "PlateScale_Scalar_Example_Adat_Set001"
#>
#> $HEADER$PlateScale_PassFlag_Example_Adat_Set001
#> [1] "PASS"
#> attr(,"raw_key")
#> [1] "PlateScale_PassFlag_Example_Adat_Set001"
#>
#> $HEADER$CalibrationReference
#> [1] "Reference_v4_Plasma_Calibrator_170261"
#> attr(,"raw_key")
#> [1] "CalibrationReference"
#>
#> $HEADER$CalPlateTailPercent_Example_Adat_Set001
#> [1] "0.1"
#> attr(,"raw_key")
#> [1] "CalPlateTailPercent_Example_Adat_Set001"
#>
#> $HEADER$PlateTailPercent_Example_Adat_Set001
#> [1] "1.2"
#> attr(,"raw_key")
#> [1] "PlateTailPercent_Example_Adat_Set001"
#>
#> $HEADER$PlateTailTest_Example_Adat_Set001
#> [1] "PASS"
#> attr(,"raw_key")
#> [1] "PlateTailTest_Example_Adat_Set001"
#>
#> $HEADER$PlateScale_Scalar_Example_Adat_Set002
#> [1] "1.09915270"
#> attr(,"raw_key")
#> [1] "PlateScale_Scalar_Example_Adat_Set002"
#>
#> $HEADER$PlateScale_PassFlag_Example_Adat_Set002
#> [1] "PASS"
#> attr(,"raw_key")
#> [1] "PlateScale_PassFlag_Example_Adat_Set002"
#>
#> $HEADER$CalPlateTailPercent_Example_Adat_Set002
#> [1] "2.6"
#> attr(,"raw_key")
#> [1] "CalPlateTailPercent_Example_Adat_Set002"
#>
#> $HEADER$PlateTailPercent_Example_Adat_Set002
#> [1] "4.2"
#> attr(,"raw_key")
#> [1] "PlateTailPercent_Example_Adat_Set002"
#>
#> $HEADER$PlateTailTest_Example_Adat_Set002
#> [1] "PASS"
#> attr(,"raw_key")
#> [1] "PlateTailTest_Example_Adat_Set002"
#>
#>
#> $COL_DATA
#> $COL_DATA$Name
#> [1] "SeqId"
#> [2] "SeqIdVersion"
#> [3] "SomaId"
#> [4] "TargetFullName"
#> [5] "Target"
#> [6] "UniProt"
#> [7] "EntrezGeneID"
#> [8] "EntrezGeneSymbol"
#> [9] "Organism"
#> [10] "Units"
#> [11] "Type"
#> [12] "Dilution"
#> [13] "PlateScale_Reference"
#> [14] "CalReference"
#> [15] "Cal_Example_Adat_Set001"
#> [16] "ColCheck"
#> [17] "CalQcRatio_Example_Adat_Set001_170255"
#> [18] "QcReference_170255"
#> [19] "Cal_Example_Adat_Set002"
#> [20] "CalQcRatio_Example_Adat_Set002_170255"
#> attr(,"raw_key")
#> [1] "!Name"
#>
#> $COL_DATA$Type
#> [1] "String" "String" "String" "String" "String" "String" "String"
#> [8] "String" "String" "String" "String" "String" "String" "String"
#> [15] "String" "String" "String" "String" "String" "String"
#> attr(,"raw_key")
#> [1] "!Type"
#>
#>
#> $ROW_DATA
#> $ROW_DATA$Name
#> [1] "PlateId" "PlateRunDate"
#> [3] "ScannerID" "PlatePosition"
#> [5] "SlideId" "Subarray"
#> [7] "SampleId" "SampleType"
#> [9] "PercentDilution" "SampleMatrix"
#> [11] "Barcode" "Barcode2d"
#> [13] "SampleName" "SampleNotes"
#> [15] "AliquotingNotes" "SampleDescription"
#> [17] "AssayNotes" "TimePoint"
#> [19] "ExtIdentifier" "SsfExtId"
#> [21] "SampleGroup" "SiteId"
#> [23] "TubeUniqueID" "CLI"
#> [25] "HybControlNormScale" "RowCheck"
#> [27] "NormScale_20" "NormScale_0_005"
#> [29] "NormScale_0_5" "ANMLFractionUsed_20"
#> [31] "ANMLFractionUsed_0_005" "ANMLFractionUsed_0_5"
#> [33] "Age" "Sex"
#> attr(,"raw_key")
#> [1] "!Name"
#>
#> $ROW_DATA$Type
#> [1] "String" "String" "String" "String" "String" "String" "String"
#> [8] "String" "String" "String" "String" "String" "String" "String"
#> [15] "String" "String" "String" "String" "String" "String" "String"
#> [22] "String" "String" "String" "String" "String" "String" "String"
#> [29] "String" "String" "String" "String" "String" "String"
#> attr(,"raw_key")
#> [1] "!Type"
#>
#>
#> $TABLE_BEGIN
#> [1] "example_data10.adat"
#>
header$file_specs
#> $empty_adat
#> [1] FALSE
#>
#> $table_begin
#> [1] 45
#>
#> $col_meta_start
#> [1] 46
#>
#> $col_meta_shift
#> [1] 35
#>
#> $data_begin
#> [1] 66
#>
#> $old_adat
#> [1] FALSE
#>
header$row_meta
#> [1] "PlateId" "PlateRunDate"
#> [3] "ScannerID" "PlatePosition"
#> [5] "SlideId" "Subarray"
#> [7] "SampleId" "SampleType"
#> [9] "PercentDilution" "SampleMatrix"
#> [11] "Barcode" "Barcode2d"
#> [13] "SampleName" "SampleNotes"
#> [15] "AliquotingNotes" "SampleDescription"
#> [17] "AssayNotes" "TimePoint"
#> [19] "ExtIdentifier" "SsfExtId"
#> [21] "SampleGroup" "SiteId"
#> [23] "TubeUniqueID" "CLI"
#> [25] "HybControlNormScale" "RowCheck"
#> [27] "NormScale_20" "NormScale_0_005"
#> [29] "NormScale_0_5" "ANMLFractionUsed_20"
#> [31] "ANMLFractionUsed_0_005" "ANMLFractionUsed_0_5"
#> [33] "Age" "Sex"
head(as.data.frame(header$Col.Meta))
#> SeqId SeqIdVersion SomaId
#> 1 10000-28 3 SL019233
#> 2 10001-7 3 SL002564
#> 3 10003-15 3 SL019245
#> 4 10006-25 3 SL019228
#> 5 10008-43 3 SL019234
#> 6 10011-65 3 SL019246
#> TargetFullName Target UniProt
#> 1 Beta-crystallin B2 CRBB2 P43320
#> 2 RAF proto-oncogene serine/threonine-protein kinase c-Raf P04049
#> 3 Zinc finger protein 41 ZNF41 P51814
#> 4 ETS domain-containing protein Elk-1 ELK1 P19419
#> 5 Guanylyl cyclase-activating protein 1 GUC1A P43080
#> 6 Inositol polyphosphate 5-phosphatase OCRL-1 OCRL Q01968
#> EntrezGeneID EntrezGeneSymbol Organism Units Type Dilution
#> 1 1415 CRYBB2 Human RFU Protein 20
#> 2 5894 RAF1 Human RFU Protein 20
#> 3 7592 ZNF41 Human RFU Protein 0.5
#> 4 2002 ELK1 Human RFU Protein 20
#> 5 2978 GUCA1A Human RFU Protein 20
#> 6 4952 OCRL Human RFU Protein 20
#> PlateScale_Reference CalReference Cal_Example_Adat_Set001 ColCheck
#> 1 687.4 687.4 1.01252025 PASS
#> 2 227.8 227.8 1.01605709 PASS
#> 3 126.9 126.9 0.95056180 PASS
#> 4 634.2 634.2 0.99607350 PASS
#> 5 585.0 585.0 0.94051447 PASS
#> 6 2807.1 2807.1 1.05383489 PASS
#> CalQcRatio_Example_Adat_Set001_170255 QcReference_170255
#> 1 1.008 505.4
#> 2 0.970 223.9
#> 3 1.046 119.6
#> 4 1.042 667.2
#> 5 1.036 587.5
#> 6 0.975 2617.6
#> Cal_Example_Adat_Set002 CalQcRatio_Example_Adat_Set002_170255
#> 1 1.01476233 1.067
#> 2 1.03686846 1.007
#> 3 1.15258856 0.981
#> 4 0.93581231 1.026
#> 5 0.96201283 0.998
#> 6 1.03133955 1.013